On the MAF, I don't think you should have this problem. I'm sure there is a cure, but I don't know what it is. My thought is that it should run but show a code. Now maybe...it should be going into a limp mode with a code set. I do know this, when I read the forums about "MAF fail" whether intentional or not, there can be complications. You should be able to make your engine run without a MAF sensor, but you may have to do something in the tune.

As far as the tune file looking different, look at the "edit" column in the main view. At the bottom there is a box called "view". You'll see more boxes/tables if the "advanced" option is checked. Hopefully that's it.

As I said, I'm no tuner. I'm just trying to be like a sponge to learn little things as I complete my build and fire it for the first time. I have a gen4 engine which is a bit different from the gen3 you have, so most of my learning and demo stuff has concentrated on that.

Along with 55moredoor's suggestion of the HPTuners forum, there is a pretty good forum on tuning at ls1tech.com, look at the subforum on "computer diagnostics and tuning".

I'm sure that several here including me are interested in what you discover to fix your problems.

yes i found the advance setting...
its kinda funny , i must have figured that one out a while back when i was messing around with my tahoe.. then forgot..
so now they all show up advanced on my laptop...

maf..yeah, i think its something in the tune as well....
every little change seems to create a domino effect..

i try to absorb as much as possible also,
just dont seem to retain as well as i use to any more...

i cant leave things alone untill i'll figure it out...
could take awhile, but i'll get there.....

If you are new to HPTuners, (as I am) take a look at this channel. This guy walks you through everything from start to finish, no fluff, no drama, no useless crap that a lot of the youtube stuff gives you.

9 part series that he is updating as he goes, walks you through the tables and how they relate.